Making holes in a mesh
You could use a couple different methods:
Boolean modifier:

Add a boolean modifier on the object you want to cut a hole in,

Create an object to &quot;subtract&quot; from the main object

Set that object in the boolean modifier. You can press E while hovering over the object selection field to set the field by clicking on an object in the 3D view.



knife project tool:

Add a circle or some other object to define the outline of the hole

With the circle selected, ⇧ Shift select the object you want to cut a hole in and enter edit mode (↹ Tab)

Select the faces you want to cut, then click knife project in the tool shelf. If you want to cut all the way through the mesh, enable Cut through in the redo panel (F6)

Then select the newly cut edges with ⎇ Alt⇧ Shift RMB and press W&gt; Bridge edge loops to connect the ends of the hole.



Face intersect tool:
This feature will be added in 2.72, but until then you can use it in the latest development builds.
This is essentially like the boolean modifier, except it works in edit mode.

Here is a nice video made by the author of this feature, explaining how it works.